Biochemical upgrading of high-protein biomass and grain products

ABSTRACT

The present invention relates to methods of upgrading biomass to provide useful chemical intermediates, fuels, amino acids, nutrients, etc. In particular examples, the biomass is a by-product of ethanol production and is mainly used as high-protein feed. Described herein are methods for upgrading such biomass, such as by implementing pre-treatment conditions and by employing fermentation conditions including modified organisms.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No.62/303,282, filed Mar. 3, 2016, which is hereby incorporated byreference in its entirety.

STATEMENT OF GOVERNMENT INTEREST

This invention was made with Government support under contract no.DE-AC04-94AL85000 awarded by the U.S. Department of Energy to SandiaCorporation. The Government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to methods of upgrading biomass to provideuseful chemical intermediates, fuels, amino acids, nutrients, etc. Inparticular examples, the biomass is a by-product of ethanol productionand is mainly used as high-protein feed. Described herein are methodsfor upgrading such biomass, such as by implementing pre-treatmentconditions and by employing fermentation conditions including modifiedorganisms.

BACKGROUND OF THE INVENTION

Production of distillers dried grains (DDGs), the primary co-product ofresidue from corn ethanol production, has dramatically increased sinceabout 2002. Despite potential utility for this product for animal feedblending, market adoption of the feedstock has been limited due toinconsistent composition and potential toxicity to livestock. Suchco-products, as well as other biomass products, can contain high valuecomponents that are difficult to recover and isolate. Accordingly, thereis a need for methods and tools to facilitate such isolation in aneffective and/or efficient manner.

SUMMARY OF THE INVENTION

The present invention relates to methods of upgrading biomass (e.g.,distillers grains, oilseed meals, etc.) in order to provide higher valueproducts, such as bioethanol, chemical intermediates, and valuable aminoacids. In particular examples, the methods herein are employed withdistillers dried grains (DDGs), a primary co-product from corn ethanolproduction with minimal market adoption. As described herein, we havedeveloped a process for biochemical upgrading of DDGs for production ofmixed alcohols (e.g., C₂₋₆ alcohols) for fuels and industrial chemicals,as well as high value amino acids (e.g., Lys, Met, His, Trp) for feedblending applications (e.g., as a fish meal replacement).

The methods herein include a pre-treatment step, as well as one or morefermentation step(s). In one non-limiting example, the pre-treatmentstep generally employs dilute acid hydrolysis, and the fermentationsteps employ E. coli fermentation modules, yielding about 40% of theorganic basis to mixed alcohols and recovery of major nutrients(nitrogen and phosphorous) as struvite.

Fermentation can be inhibited by the presence of several chemicalconstituents. For instance, the presence of excess alcohol in thefermentation product can inhibit the functionality of the organism to,e.g., break down amino acids. In another non-limiting instance, cofactorimbalance can limit fermentation, e.g., in which the lack of aparticular cofactor can result in limited yield of desired fermentationproducts. Thus, in some non-limiting methods herein, the biomass istreated in a manner to promote, rather than inhibit, fermentation, e.g.,by providing two fermentation steps, in which the first step includesremoval of excess alcohol and the second step includes break-down ofproteins or amino acids; and, e.g., by providing a genetically modifiedorganism suited for employing a cofactor that does not limitfermentation, such as an organism that is selected by direct evolutionto have a non-native cofactor specificity.

The present invention also relates to genetically modified organisms(e.g., for employment in any fermentation step described herein). Inparticular, we describe two types of genetically modified E. colistrains that were optimized for conversion of hydrolyzed carbohydratesand proteins, respectively.

The methods herein can be optimized to recover any useful component(e.g., biocomponent, intermediate, etc.). In one non-limiting example,the fermentation liquor was extracted with ethyl acetate to recover themixed alcohols at about 90% yield, and the extraction solvent wasrecovered by distillation. Further lyophilization of the extractedfermentation liquor yielded a crystalline powder enriched with highvalue amino acids. Additional details follow.

Definitions

As used herein, the term “about” means +/−10% of any recited value. Asused herein, this term modifies any recited value, range of values, orendpoints of one or more ranges.

The terms “polynucleotide” and “nucleic acid,” used interchangeablyherein, refer to a polymeric form of nucleotides of any length, eitherribonucleotides or deoxyribonucleotides. Thus, this term includes, butis not limited to, single-stranded (e.g., sense or antisense),double-stranded, or multi-stranded ribonucleic acids (RNAs),deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycolnucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids(LNAs), or hybrids thereof, genomic DNA, cDNA, DNA-RNA hybrids, or apolymer comprising purine and pyrimidine bases or other natural,chemically or biochemically modified, non-natural, or derivatizednucleotide bases. Polynucleotides can have any useful two-dimensional orthree-dimensional structure or motif, such as regions including one ormore duplex, triplex, quadruplex, hairpin, and/or pseudoknot structuresor motifs.

The term “modified,” as used in reference to nucleic acids, means anucleic acid sequence including one or more modifications to thenucleobase, nucleoside, nucleotide, phosphate group, sugar group, and/orinternucleoside linkage (e.g., phosphodiester backbone, linkingphosphate, or a phosphodiester linkage).

The term “modified,” as used in reference to amino acids, means an aminoacid including one or more modifications, such as a post-translationmodification (e.g., acetylation, methylation, phosphorylation,ubiquitination, sumoylation, ribosylation, glycosylation, acylation, orisomerization), or including a non-natural amino acid.

The term “modified,” as used in reference to a protein, means apolypeptide sequence including one or more amino acid substitution, ascompared to the reference sequence for the protein.

“Complementarity” or “complementary” or “complement” refers to theability of a nucleic acid to form hydrogen bond(s) with another nucleicacid sequence by either traditional Watson-Crick or othernon-traditional types, e.g., form Watson-Crick base pairs and/or G/Ubase pairs, “anneal”, or “hybridize,” to another nucleic acid in asequence-specific, antiparallel, manner (i.e., a nucleic acidspecifically binds to a complementary nucleic acid) under theappropriate in vitro and/or in vivo conditions of temperature andsolution ionic strength. As is known in the art, standard Watson-Crickbase-pairing includes: adenine (A) pairing with thymidine (T), adenine(A) pairing with uracil (U), and guanine (G) pairing with cytosine (C).In addition, it is also known in the art that for hybridization betweentwo RNA molecules (e.g., dsRNA), guanine (G) base pairs with uracil (U).A percent complementarity indicates the percentage of residues in anucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crickbase pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9,10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary).“Perfectly complementary” means that all the contiguous residues of anucleic acid sequence will hydrogen bond with the same number ofcontiguous residues in a second nucleic acid sequence. “Substantiallycomplementary” or “sufficient complementarity” as used herein refers toa degree of complementarity that is at least 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%. 97%, 98%, 99%, or 100% over a region of 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50,or more nucleotides, or refers to two nucleic acids that hybridize understringent conditions.

As used herein, “stringent conditions” for hybridization refer toconditions under which a nucleic acid having complementarity to a targetsequence predominantly hybridizes with the target sequence, andsubstantially does not hybridize to non-target sequences. Stringentconditions are generally sequence-dependent, and vary depending on anumber of factors. In general, the longer the sequence, the higher thetemperature at which the sequence specifically hybridizes to its targetsequence. Non-limiting examples of stringent conditions are described indetail in Tijssen (1993), Laboratory Techniques In Biochemistry AndMolecular Biology-Hybridization With Nucleic Acid Probes Part 1, SecondChapter “Overview of principles of hybridization and the strategy ofnucleic acid probe assay”, Elsevier, N.Y.

“Hybridization” refers to a reaction in which one or morepolynucleotides react to form a complex that is stabilized via hydrogenbonding between the bases of the nucleotide residues. The hydrogenbonding may occur by Watson Crick base pairing, Hoogstein binding, or inany other sequence specific manner. The complex may comprise two strandsforming a duplex structure, three or more strands forming a multistranded complex, a single self-hybridizing strand, or any combinationof these. A hybridization reaction may constitute a step in a moreextensive process, such as the initiation of PCR, or the cleavage of apolynucleotide by an enzyme. A sequence capable of hybridizing with agiven sequence is referred to as the “complement” of the given sequence.Hybridization and washing conditions are well known and exemplified inSambrook J, Fritsch E F, and Maniatis T, “Molecular Cloning: ALaboratory Manual,” Second Edition, Cold Spring Harbor Laboratory Press,Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1therein; and Sambrook J and Russell W, “Molecular Cloning: A LaboratoryManual,” Third Edition, Cold Spring Harbor Laboratory Press, Cold SpringHarbor (2001). The conditions of temperature and ionic strengthdetermine the “stringency” of the hybridization.

Hybridization requires that the two nucleic acids contain complementarysequences, although mismatches between bases are possible. Theconditions appropriate for hybridization between two nucleic acidsdepend on the length of the nucleic acids and the degree ofcomplementation, variables well known in the art. The greater the degreeof complementation between two nucleotide sequences, the greater thevalue of the melting temperature (Tm) for hybrids of nucleic acidshaving those sequences. For hybridizations between nucleic acids withshort stretches of complementarity (e.g., complementarity over 35 orless, 30 or less, 25 or less, 22 or less, 20 or less, or 18 or lessnucleotides) the position of mismatches becomes important (see Sambrooket al., supra, 11.7-11.8). Typically, the length for a hybridizablenucleic acid is at least about 10 nucleotides. Illustrative minimumlengths for a hybridizable nucleic acid are: at least about 15nucleotides; at least about 20 nucleotides; at least about 22nucleotides; at least about 25 nucleotides; and at least about 30nucleotides). Furthermore, the skilled artisan will recognize that thetemperature and wash solution salt concentration may be adjusted asnecessary according to factors such as length of the region ofcomplementation and the degree of complementation.

It is understood in the art that the sequence of polynucleotide need notbe 100% complementary to that of its target nucleic acid to bespecifically hybridizable or hybridizable. Moreover, a polynucleotidemay hybridize over one or more segments such that intervening oradjacent segments are not involved in the hybridization event (e.g., aloop structure or hairpin structure). A polynucleotide can comprise atleast 70%, at least 80%, at least 90%, at least 95%, at least 99%, or100% sequence complementarity to a target region within the targetnucleic acid sequence to which they are targeted. For example, anantisense nucleic acid in which 18 of 20 nucleotides of the antisensecompound are complementary to a target region, and would thereforespecifically hybridize, would represent 90 percent complementarity. Inthis example, the remaining noncomplementary nucleotides may beclustered or interspersed with complementary nucleotides and need not becontiguous to each other or to complementary nucleotides. Percentcomplementarity between particular stretches of nucleic acid sequenceswithin nucleic acids can be determined routinely using BLAST programs(basic local alignment search tools) and PowerBLAST programs known inthe art (Altschul S F et al., J. Mol. Biol. 1990; 215:403-10; Zhang J etal., Genome Res. 1997; 7:649-56) or by using the Gap program (WisconsinSequence Analysis Package, Version 8 for Unix, Genetics Computer Group,University Research Park, Madison Wis.), using default settings, whichuses the algorithm of Smith T F et al., Adv. Appl. Math. 1981;2(4):482-9).

By “protein,” “peptide,” or “polypeptide,” as used interchangeably, ismeant any chain of more than two amino acids, regardless ofpost-translational modification (e.g., glycosylation orphosphorylation), constituting all or part of a naturally occurringpolypeptide or peptide, or constituting a non-naturally occurringpolypeptide or peptide, which can include coded amino acids, non-codedamino acids, modified amino acids (e.g., chemically and/or biologicallymodified amino acids), and/or modified backbones.

The term “fragment” is meant a portion of a nucleic acid or apolypeptide that is at least one nucleotide or one amino acid shorterthan the reference sequence. This portion contains, preferably, at leastabout 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entirelength of the reference nucleic acid molecule or polypeptide. A fragmentmay contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400,500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 1800 or morenucleotides; or 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250,300, 350, 400, 450, 500, 550, 600, 640 amino acids or more. In anotherexample, any polypeptide fragment can include a stretch of at leastabout 5 (e.g., about 10, about 20, about 30, about 40, about 50, orabout 100) amino acids that are at least about 40% (e.g., about 50%,about 60%, about 70%, about 80%, about 90%, about 95%, about 87%, about98%, about 99%, or about 100%) identical to any of the sequencesdescribed herein can be utilized in accordance with the invention. Incertain embodiments, a polypeptide to be utilized in accordance with theinvention includes 2, 3, 4, 5, 6, 7, 8, 9, 10, or more mutations (e.g.,one or more conservative amino acid substitutions, as described herein).In yet another example, any nucleic acid fragment can include a stretchof at least about 5 (e.g., about 7, about 8, about 10, about 12, about14, about 18, about 20, about 24, about 28, about 30, or more)nucleotides that are at least about 40% (about 50%, about 60%, about70%, about 80%, about 90%, about 95%, about 87%, about 98%, about 99%,or about 100%) identical to any of the sequences described herein can beutilized in accordance with the invention.

The term “conservative amino acid substitution” refers to theinterchangeability in proteins of amino acid residues having similarside chains (e.g., of similar size, charge, and/or polarity). Forexample, a group of amino acids having aliphatic side chains consists ofglycine (Gly, G), alanine (Ala, A), valine (Val, V), leucine (Leu, L),and isoleucine (Ile, I); a group of amino acids havingaliphatic-hydroxyl side chains consists of serine (Ser, S) and threonine(Thr, T); a group of amino acids having amide containing side chainsconsisting of asparagine (Asn, N) and glutamine (Gln, Q); a group ofamino acids having aromatic side chains consists of phenylalanine (Phe,F), tyrosine (Tyr, Y), and tryptophan (Trp, W); a group of amino acidshaving basic side chains consists of lysine (Lys, K), arginine (Arg, R),and histidine (His, H); a group of amino acids having acidic side chainsconsists of glutamic acid (Glu, E) and aspartic acid (Asp, D); and agroup of amino acids having sulfur containing side chains consists ofcysteine (Cys, C) and methionine (Met, M). Exemplary conservative aminoacid substitution groups are valine-leucine-isoleucine,phenylalanine-tyrosine, lysine-arginine, alanine-valine, glycine-serine,glutamate-aspartate, and asparagine-glutamine.

As used herein, when a polypeptide or nucleic acid sequence is referredto as having “at least X % sequence identity” to a reference sequence,it is meant that at least X percent of the amino acids or nucleotides inthe polypeptide or nucleic acid are identical to those of the referencesequence when the sequences are optimally aligned. An optimal alignmentof sequences can be determined in various ways that are within the skillin the art, for instance, the Smith Waterman alignment algorithm (SmithT F et al., J. Mol. Biol. 1981; 147:195-7) and BLAST (Basic LocalAlignment Search Tool; Altschul S F et al., J. Mol. Biol. 1990;215:403-10). These and other alignment algorithms are accessible usingpublicly available computer software such as “Best Fit” (Smith T F etal., Adv. Appl. Math. 1981; 2(4):482-9) as incorporated into GeneMatcherPlus™ (Schwarz and Dayhof, “Atlas of Protein Sequence and Structure,”ed. Dayhoff, M. O., pp. 353-358, 1979), BLAST, BLAST-2, BLAST-P,BLAST-N, BLAST-X, WU-BLAST-2, ALIGN, ALIGN-2, CLUSTAL, T-COFFEE, MUSCLE,MAFFT, or Megalign (DNASTAR). In addition, those skilled in the art candetermine appropriate parameters for measuring alignment, including anyalgorithms needed to achieve optimal alignment over the length of thesequences being compared. In general, for polypeptides, the length ofcomparison sequences can be at least five amino acids, preferably 10,20, 30, 40, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 250, 300, 400,500, 600, 700, or more amino acids, up to the entire length of thepolypeptide. For nucleic acids, the length of comparison sequences cangenerally be at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 125, 150,175, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200,1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, or morenucleotides, up to the entire length of the nucleic acid molecule. It isunderstood that for the purposes of determining sequence identity whencomparing a DNA sequence to an RNA sequence, a thymine nucleotide isequivalent to a uracil nucleotide.

By “substantial identity” or “substantially identical” is meant apolypeptide or nucleic acid sequence that has the same polypeptide ornucleic acid sequence, respectively, as a reference sequence, or has aspecified percentage of amino acid residues or nucleotides,respectively, that are the same at the corresponding location within areference sequence when the two sequences are optimally aligned. Forexample, an amino acid sequence that is “substantially identical” to areference sequence has at least about 50%, 60%, 70%, 75%, 80%, 85%, 90%,95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the referenceamino acid sequence. For polypeptides, the length of comparisonsequences will generally be at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 25, 50, 75, 90, 100, 150, 200, 250, 300, or 350contiguous amino acids (e.g., a full-length sequence). For nucleicacids, the length of comparison sequences will generally be at least 5,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25contiguous nucleotides (e.g., the full-length nucleotide sequence).Sequence identity may be measured using sequence analysis software onthe default setting (e.g., Sequence Analysis Software Package of theGenetics Computer Group, University of Wisconsin Biotechnology Center,1710 University Avenue, Madison, Wis., 53705). Such software may matchsimilar sequences by assigning degrees of homology to varioussubstitutions, deletions, and other modifications.

A “vector” or “expression vector” is a replicon, such as plasmid, phage,virus, or cosmid, to which another nucleic acid segment, i.e., an“insert”, may be attached so as to bring about the replication of theattached segment in a cell.

An “expression cassette” comprises a nucleic acid coding sequenceoperably linked, as defined herein, to a promoter sequence, as definedherein.

“Operably linked” or “operatively linked” or “operatively associatedwith,” as used interchangeably, refers to a juxtaposition wherein thecomponents so described are in a relationship permitting them tofunction in their intended manner. For instance, a promoter is operablylinked to a coding sequence if the promoter affects its transcription orexpression. A nucleic acid molecule is operatively linked or operablylinked to, or operably associated with, an expression control sequencewhen the expression control sequence controls and regulates thetranscription and translation of nucleic acid sequence. The term“operatively linked” includes having an appropriate start signal (e.g.,ATG) in front of the nucleic acid sequence to be expressed andmaintaining the correct reading frame to permit expression of thenucleic acid sequence under the control of the expression controlsequence and production of the desired product encoded by the nucleicacid sequence. If a gene that one desires to insert into a recombinantDNA molecule does not contain an appropriate start signal, such a startsignal can be inserted in front of the gene.

As used herein, the terms “top,” “bottom,” “upper,” “lower,” “above,”and “below” are used to provide a relative relationship betweenstructures. The use of these terms does not indicate or require that aparticular structure must be located at a particular location in theapparatus.

Other features and advantages of the invention will be apparent from thefollowing description and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1C shows exemplary process flow diagrams for upgrading biomass.Provided are (A) an exemplary process 10 including processing pathwaysand (B) another exemplary process 100 including a pre-treatment step121,122 prior to each fermentation step 131,132. The unit operations ofthe process are depicted as designated boxes, where inputs and outputsare designated by arrows leading either into or away from a box,respectively. Also provided is (C) an exemplary process 1000 with anoptional second pre-treatment step 1022.

FIG. 2 shows another exemplary process flow diagram. Provided is anexemplary process 200 including inputs and outputs designated by arrowsleading either into or away from a box, respectively.

FIG. 3A-3D shows exemplary processes with various sub-steps. Providedare (A) an exemplary process including sub-steps for the pre-treatment310 and fermentation 320 steps; (B) an exemplary process including adistillation/extraction step 3005 between the pre-treatment 3003 andfermentation 3004 steps; (C) another exemplary process including a firstpre-treatment step 3103 and a subsequent distillation/extraction step3105 to separate a biomass solid (e.g., a bioresidue); and (D) yetanother exemplary process including distillation/extraction steps3505,3605 subsequent to each fermentation step 3504,3604.

FIG. 4A-4B shows comparative technoeconomic potential of varioushigh-protein feedstocks, including dried distillers grains with solubles(DDGS). Provided are (A) a comparison of net theoretical amino acidyields for various biomass and (B) a comparison of unutilized high valueamino acids for various biomass. The asterisk in (A) indicates thatremineralized ammonia (as NH₄MgPO₄) was included in the mass balance.

FIG. 5 shows the effect of redox cofactor engineering to produce variousgenetically engineered organism strains. Provided is a graph showing theconcentration of fusel butanol produced by various redox mutant strainsin the presence of an amino acid mixture. Redox mutant strains includeAY1, AY2, AY3, AY5, VY2, VY3, VY5, IA, and IV, as described herein,which were compared to the wild-type (WT) strain.

FIG. 6 shows an exemplary process flow diagram for upgrading biomass,such as DDGs.

FIG. 7 shows another exemplary process flow diagram for furtheroptimization.

FIG. 8 shows carbohydrate hydrolysis and ethanol yields, in which theprocess included dilute acid pre-treatment and fermentation.

FIG. 9 shows protein hydrolysis and fusel alcohol yields, in which theprocess included dilute acid pre-treatment, enzymatic pre-treatment(e.g., protease digestion), and fermentation.

FIG. 10A-10G shows the effects of cofactor engineering for E. colialcohol dehydrogenase (YqhD). Provided are (A) an image showingstructural alignment of the NADP-binding pocket for YqhD and (B) a graphshowing mutant enzyme activity employing cofactor NADH, as compared toWT YqhD. Also provided are polypeptide sequences for E. coli YqhD,including sequences for (C) wild-type (SEQ ID NO: 1) having Gly atpositions 37-39 and Ser at position 40; (D) YqhD mutant 1 including amutation at position 39 (SEQ ID NO:2), in which Xaa at position 39 canbe any useful amino acid substitution (e.g., Ile, Tyr, Val, Leu, Phe, orany other conservative amino acid substitution described herein); (E)YqhD mutant 2 including a mutation at position 40 (SEQ ID NO:3), inwhich Xaa at position 40 can be any useful amino acid substitution(e.g., Pro, Arg, His, Lys, Trp, or any other conservative amino acidsubstitution described herein); (F) YqhD mutant 3 including a mutationat both positions 39 and 40 (SEQ ID NO:4), in which Xaa at position 39and 40 can be any useful amino acid substitution (e.g., Ile at position39 and Arg at position 40; Tyr at position 39 and His at position 40; aswell as any other conservative amino acid substitution describedherein); and (G) YqhD mutant 3 including a mutation at positions 39 and40 (SEQ ID NO:5) with an optional substitution at positions 37 and 38,in which Xaa at position 39 and 40 can be any useful amino acidsubstitution (e.g., Ile at position 39 and Arg at position 40; Tyr atposition 39 and His at position 40; as well as any other conservativeamino acid substitution described herein). In some instances, the mutant(e.g., of SEQ ID NO:2-5) includes Gly, Ile, Tyr, Val, Leu, Phe, or anyother conservative amino acid substitution described herein, forpositions 37, 38, and 39; and Ser, Pro, Arg, His, Lys, Trp, or any otherconservative amino acid substitution described herein for position 40(e.g., in which position 39 and/or 40 includes an amino acidsubstitution as compared to the wild-type sequence, e.g., SEQ ID NO: 1).

FIG. 11A-11B provides polypeptide sequences for E. coli ketol-acidreductoisomerase IlvC, including sequences for (A) wild-type (SEQ IDNO:6) having Ala at position 71, Arg at position 76, Ser at position 78,Gln at position 110, Asp at position 146, Gly at position 185, and Lysat position 433; and (B) IlvC mutant including a mutation at positions71, 76, 78, and/or 110 (SEQ ID NO:7). Exemplary substitutions includeSer or Thr at position 71, Asp or Glu at position 76, Asp or Glu atposition 78, and/or Val or Ala or Leu or Ile at position 110, as well asany other conservative amino acid substitution described herein.Optionally, SEQ ID NO:7 can include other substitutions, including Glyor Ala at position 146, Arg or Lys at position 185, and/or Glu or Asp atposition 433.

FIG. 12A-12B shows the effect of adding native cofactor NADPH on yieldof butanol for protein bioconversion. Provided are (A) a graph showingthe effects of NADPH addition on the produced concentration fuselbutanol under anaerobic fermentation conditions and (B) a graph showingthe improvement of fusel butanol yield after 24 hours and 120 hours.

FIG. 13A-13C shows bioconversion of algal protein hydrolysates intofusel butanol by engineered mutant strains. Provided are (A) a graphshowing fermentation performance of engineered mutant strains on anamino acid mixture; (B) a graph showing bioconversion of two algalprotein hydrolysates (ATP3 or ODU) into fusel butanol employing eitheran engineered mutant strain AY3 or a wild-type strain YH83 (“WT”); and(C) a graph showing consumption of two algal protein hydrolysates (ATP3or ODU) by engineered mutant strain AY3 after 72 hours.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to the upgrading biomass (e.g.,high-protein biomass) into ethanol and other useful intermediates, suchas amino acids, bioresidue, etc. Such intermediates, in turn, can besuitable for any useful industrial process, such as downstream refining,e.g., using known petrochemical facilities and processes. In particularembodiments, an exemplary process of the invention combinespre-treatment of the biomass to solubilize and hydrolyze thecarbohydrate and protein fractions; followed by fermentation andoptional distillation/extraction to recover useful alcohols, aminoacids, etc. In some embodiments, the process employs biochemical stepsto effectively solubilize, hydrolyze, and/or degrade components of thebiomass (e.g., by employing a genetically engineered organism, such asany herein).

An exemplary process 10 is shown in FIG. 1A. A biomass 11 is provided,typically including fractions of proteins, carbohydrates, and/or lipids(collectively, biocomponents).

Further treatment steps can be employed to breakdown these biocomponentsinto useful residuals. Exemplary steps include pre-treatment 12 (e.g.,employing dilute acid and/or enzymes in sequential or simultaneoussteps) to hydrolyze and/or solubilize the biocomponents (e.g., such asto provide one or more sugars, including glucose, xylose, arabinose,etc.); as well as fermentation and optional distillation 13 to degradethe biocomponents into one or more alcohols (e.g., ethanol, 1-propanol,isobutanol, 1-butanol, 2-methyl-1-butanol, 3-methyl-1-butanol,2-phenylethanol, isopentanol, etc.), amino acids, and amines.

Fermentation is typically employed to degrade sugars, carbohydrates, andproteins into further, smaller chemical components, such as alcohols,amino acids, and amines. In use, fermentation employs one or moreorganisms, such as bacteria or yeast, to degrade these biocomponents.Exemplary organisms are described herein (e.g., bacteria such as E.coli, as well as mutant forms that are selected to degrade sugars,carbohydrates, and/or proteins in a selective, specific, and/or usefulmanner). Typically, such organisms do not degrade lipids. Thus,conventional fermentation is usually conducted in aqueous, non-lipidsamples. In some embodiments of the invention herein, organisms can begenetically modified to convert lipids. In other embodiments of theinvention herein, the fermentation step includes use of one or morelipids, lipid vesicles, and/or lipid micelles within the fermentationbroth.

After fermentation, one or more by-products (e.g., minerals, nutrients,water, etc.) can be optionally removed from any of the fractions.Nutrients, by-products, and water can be extracted within any point ofthe processing stream and with any useful mixture obtained within theprocessing stream. Such extraction steps can include removal ofby-products from the fermentation broth or a portion thereof, deliveryof nitrogen (N) and/or phosphorous (P) sources (e.g., as a salt, amineral, etc.), and/or delivery of water. Any fractions obtained fromthese biocomponents can be processed to recovery nutrients (e.g., Nand/or P) in any useful form, such as a protonated form (e.g., ammoniafor capturing N), an oxide form (e.g., phosphate for capturing P), asalt form, and/or a mineral (e.g., struvite for capturing N and P).

In other examples, after the fermentation step, the aqueous andnon-aqueous (e.g., lipid) fractions are phase-separated and processed inparallel steps. For instance, the non-aqueous fraction, including abioresidue (e.g., a low nitrogen organic residue) composed of one ormore lipids, can be treated by way of hydrothermal liquefaction (HTL) 14to provide a biocrude oil. Any solid residuals, such as ash or char, canbe removed after liquefaction. Any liquid residuals can be furtherprocessed to recover 15 any useful nutrients.

In another example, the aqueous fraction (e.g., including water-solublecomponents) can be distilled to remove alcohols (e.g., along withneutral lipids). Optionally, such fractions or extracted fractions canbe further processed to recover any useful nutrients 15 (e.g., forrecovering nitrogen and/or phosphorus) or usable water 16 (e.g., for usein multi-pass recycle operations) in the aqueous phase, as well as toextract any lipids present in the aqueous phase.

Any useful thermochemical process can be employed to process abioresidue into a biocrude oil. Exemplary thermochemical processesinclude liquefaction, pyrolysis, gasification, and/or combustion in theoptional presence of one or more catalysts. Experimental conditions(e.g., temperature, pressure, air composition, reactants, reagents,etc.) can be optimized in any useful manner to achieve the desiredbiocrude oil with appropriate viscosity, color, oxygen content, nitrogencontent, etc. In addition, the biocrude oil can be further upgraded intobiofuels, such as by use of hydrotreatment (e.g., as described herein).

Yet another upgrading process 100 is shown in FIG. 1B, which provides apre-treatment step 121,122 prior to each fermentation step 131,132.Overall, the exemplary non-limiting process 100 includes providing 111 abiomass (e.g., distillers grain); pre-treating 121 the biomass (e.g.,with a dilute acid pre-treatment) and optionally separating a biomasssolid; fermenting 131 the carbohydrate fraction (e.g., including one ormore sugars) of the biocomponents with a genetically engineered organismuseful for degrading carbohydrates (e.g., thereby producing ethanol)with optional distillation (e.g., of the produced ethanol); pre-treating122 the biomass (e.g., with one or more enzymes); fermenting 132 theprotein fraction (e.g., including one or more proteins, peptides, and/oramino acids) of the biocomponents with a genetically engineered organismuseful for degrading amino acids (e.g., thereby producing one or moremixed alcohols, lipids, amino acids, and/or amines) with optionaldistillation (e.g., of the produced mixed alcohols); liquefying 140 anyresidual or fraction of a fermentation product (e.g., by way ofhydrothermal liquefaction, thereby producing a biocrude); and recovering150 any residual or fraction of a fermentation product (e.g., therebyproducing a nutrient, such as nitrogen, phosphorous, magnesium etc.).

Pre-treatment can be employed to release various biocomponents frombiomass that can be difficult to process. In addition, the process caninclude separated fermentation steps, in which each step can beoptimized or selected to degrade a particular type of biocomponent. Asseen in FIG. 1B, the process 100 includes a first fermentation step 131useful for degrading sugar and carbohydrate components, therebyproducing ethanol; and a second fermentation step 132 useful fordegrading protein and amino acid components, thereby producing mixedalcohols, amines, and released amino acids.

Each pre-treatment step can be optionally followed by a separation step,such as by separating one or more solid components from a liquidportion. The liquid portion can be further processed (e.g., byfermentation), and the separated solid components can be re-introducedinto the process at a later step in the processing pathway (e.g.,enzymatic pre-treatment).

A second pre-treatment step can be optional. FIG. 1C shows anotherexemplary upgrading process 1000 that includes providing 1011 a biomass(e.g., distillers grain); pre-treating 1021 the biomass (e.g., with adilute acid pre-treatment); fermenting 1031 the carbohydrate fraction(e.g., including one or more sugars) with optional distillation (e.g.,of the produced ethanol); optionally pre-treating 1022 the biomass(e.g., with one or more enzymes); fermenting 1032 the protein fraction(e.g., including one or more proteins, peptides, and/or amino acids)with optional distillation (e.g., of the produced mixed alcohols);liquefying 1040 any residual or fraction of a fermentation product(e.g., by way of hydrothermal liquefaction, thereby producing abiocrude); and recovering 1050 any residual or fraction of afermentation product (e.g., thereby producing a nutrient, such asnitrogen, phosphorous, magnesium etc.)

Another exemplary conversion process 200 is shown in FIG. 2, whichprovides various inputs and outputs during the process. As can be seen,the process 200 includes a first step of providing 211 a biomass (e.g.,distillers grain), which can then be pre-treated 221. This pre-treatmentstep 221 can include any useful input, e.g., water, one or more acids(e.g., dilute or strong H₂SO₄), a neutralizer (e.g., a base, such asNaOH), and/or one or more enzymes (e.g., a protease or a proteasecocktail). The fermentation step 231 results in conversion ofcarbohydrates into one or more smaller or simpler components (e.g.,alcohols) by employing an organism strain useful for sugar fermentation.A second pretreatment step 222 generally includes one or more enzymes,and a second fermentation step 232 results in conversion of proteinsinto one or more smaller or simpler components (e.g., alcohols, aminoacids, ketoacids, and/or amines) by employing an organism strain usefulfor protein fermentation. Such smaller or simpler components can befurther purified (e.g., extracted, distilled, precipitated, etc.) toprovide pharmaceutical intermediates, chemicals, chemical/biochemicalprecursors, building blocks, reagents, and/or intermediates.

A distillation step (e.g., conducted after one fermentation step orafter each fermentation step) can result in the separation of volatilefraction(s) from the less volatile fraction(s), resulting in, e.g., afraction including one or more alcohols or mixtures thereof, and anotherfraction including a predominantly non-aqueous, lipid phase (e.g., abioresidue). The fraction including alcohol(s) can be further purifiedto provide bioethanol.

Optionally, the bioresidue can be thermally treated at a temperaturesufficient to separate volatile lipids from solid residuals, such as byway of hydrothermal liquefaction 240, to produce a liquefied mixture.This liquefied mixture can include biocrude oil, ash, biochar, and othercomponents. The biocrude oil, in turn, can be further processed, e.g.,by way of hydrotreatment with an input of hydrogen, to produce anyuseful biofuel, such as biodiesel, naphtha, or light hydrocarbons. Othercomponents from the liquefied mixture can be phase separated to extractthe solid residuals. This liquid phase can be further processed fornutrient and water recovery 250.

Any useful biomass can be employed. Exemplary biomass include distillersgrains or co-products (e.g., wet distillers grains (WDGs), drieddistillers grains (DDGs), dried distillers grains with solubles (DDGS),fatty acids from oil hydrolysis, lipids from evaporation of thinstillage, syrup, distillers grains, distillers grains with or withoutsolubles, solids from a mash before fermentation, solids from a wholestillage after fermentation, biodiesel, and acyl glycerides), oilseedmeals (e.g., soybean meal or canola meal), feeds (e.g., alfalfa meal,cottonseed meal, DDGS, rice bran, or wheat bran), yeast (e.g.,extracts), algae (e.g., Nannochloropsis, wastewater algae, or anydescribed herein), cereal by-products (e.g., whey), etc.

Pre-Treatment of the Biomass

Pre-treatment can be used to convert constituents within the biomassinto various biocomponents (e.g., proteins, carbohydrates, fatty acids,and/or lipids). Such biocomponents can be pre-treated to obtain moresolubilized or hydrolyzed constituents, such as amino acids or sugars(e.g., glucose). For instance, carbohydrates within the biomass can bepre-treated and, thereby, be converted into a sugar and/or an alcohol,such as glucose, fucose, galactose, xylose, mannose, mannitol, ethanol,butanol, and/or pentanol. In another instance, proteins within thebiomass can be treated and, thereby, hydrolyzed and converted into aminoacids. Such amino acids, in turn, can be fermented to produce one ormore mixed alcohols and amines. In addition, one or more extractiontechniques can be applied to separate the protein/carbohydrate fractionfrom other constituents. Such extraction techniques can include, e.g.,use of one or more ionic liquids to selectively extract a particularfraction.

Pre-treatment can include the use of one or more acids, bases,oxidizers, reducers, and/or enzymes. Exemplary pre-treatment conditionsinclude strong and/or dilute acid hydrolysis (e.g., with H₂SO₄ and/orHCl), base hydrolysis or neutralization (e.g., with NaOH), heattreatment, sonication, and/or enzyme degradation (e.g., with one or moreproteases, such as endoproteases, exoproteases, serine proteases (e.g.,subtilisin, also known as alcalase), aminopeptidases, carboxypeptidases,endoglucanases, cellobiohydrolases, glycoside hydrolases (e.g.,lysozyme), endoglucanases, glucanases, endoxyalanases, pectinases,sulfatases (e.g., arylsulfatases), cellulases, xylanases, as well asmixtures thereof, such that available as commercially availablePronase®, a mixture of proteolytic enzymes that are produced in theculture supernatant of Streptomyces griseus K-1).

Fermentation

Fermentation conditions generally include the use of one or moreorganisms to convert starting reactants (e.g., biocomponents, such ascarbohydrates, proteins, sugars, amino acids, etc.) into alcohol andother co-products. Fermentation can include degradation of carbohydratesinto alcohol in the presence of one or more organisms. Such conditionscan also release mixed alcohols and nitrogen from degradation ofprotein, which can contain up to about 90% of the nitrogen in a biomass.In this manner, fermentation provides useful biofuels and intermediates(e.g., alcohols). Furthermore, released nitrogen can be recovered andrecycled.

For fermentation, any useful organisms can be employed, such as one ormore bacteria (e.g., Escherichia, such as E. coli; Zymobacter, such asZ. palmae; or Zymomonas, such as Z. mobilis) and one or more yeast(e.g., Saccharomyces, such as S. cerevisiae), including mutant formsthereof, including those that deaminate protein hydrolysates (e.g., intoketoacids, tricarboxylic acid cycle intermediates, etc.), that convertproteins to alcohols (e.g., to C4 or C5 alcohols), and/or that lack oneor more quorum-sensing genes (e.g., genes luxS or lsrA), such as thosedescribed in Atsumi S et al., “Non-fermentative pathways for synthesisof branched-chain higher alcohols as biofuels,” Nature 2008; 451:86-90;and Huo Y X et al., “Conversion of proteins into biofuels by engineeringnitrogen flux,” Nat. Biotechnol. 2011; 29(4):346-51, which isincorporated herein by reference in its entirety; yeast (e.g.,Saccharomyces, such as S. cerevisiae and S. uvarum); and fungi (e.g.,Aspergillus, such as A. niger, A. terreus, and A. fumigatus).

In one instance, fermentation is conducted in the presence of one ormore organisms useful for sugar or carbohydrate fermentation. Suchorganisms can include those selected by directed evolution to employ anyuseful sugar substrate, to have enhanced alcohol tolerance, and/or tohave increased activity. Exemplary organisms include E. coli KO11, E.coli LY01, E. coli SZ110, E. coli LY168, Z. mobilis mobilis AX101, S.cerevisiae 424A(LNH-ST), and S. cerevisiae ATCC 96581.

In another instance, fermentation is conducted in the presence of one ormore organisms useful for protein fermentation. Such organism caninclude those selected by directed evolution to switch cofactorspecificity, to deaminate protein hydrolysates, and/or to reducecompeting pathways. Exemplary organisms include those having mutantsforms of one or more enzymes, such as YqhD and/or IlvC mutants to switchcofactor specificity, transhydrogenase overexpression in E. coli PntAB,alcohol dehydrogenase mutants (e.g., mutants of AdhE, AdhP, EutG, YiaY,YqhD, and/or YjgB), and/or ketol-acid isomerase mutants (e.g., mutantsof IlvC, IlvD, IlvH, and/or IlvA), as well as any described inBrinkmann-Chen S et al., “General approach to reversing ketol-acidreductoisomerase cofactor dependence from NADPH to NADH,” Proc. Nat'lAcad. Sci. USA 2013; 110(27): 10946-51; and Bastian S et al.,“Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enableanaerobic 2-methylpropan-1-ol production at theoretical yield inEscherichia coli,” Metab. Eng. 2011; 13(3):345-52, each of which isincorporated herein by reference in its entirety.

Exemplary mutants include a YqhD mutant (e.g., a mutant having apolypeptide sequence with at least one amino acid substitution, ascompared to wild-type YqhD (e.g., such as SEQ ID NO:1 in FIG. 10C). Inone non-limiting example, the YqhD mutant has a polypeptide sequence ofSEQ ID NO:2 (FIG. 10D), or a fragment thereof, in which Xaa at position39 is Ile, Tyr, Val, Leu, Phe, or any other conservative amino acidsubstitution described herein. In another non-limiting example, the YqhDmutant has a polypeptide sequence of SEQ ID NO:3 (FIG. 10E), or afragment thereof, in which Xaa at position 40 is Pro, Arg, His, Lys, Trpor any other conservative amino acid substitution described herein.

In yet another non-limiting example, the YqhD mutant has a polypeptidesequence of SEQ ID NO:4 (FIG. 10F), or a fragment thereof, in which Xaaat position 39 is Ile, Tyr, Val, Leu, Phe, or any other conservativeamino acid substitution described herein; and in which Xaa at position40 is Pro, Arg, His, Lys, Trp or any other conservative amino acidsubstitution described herein. In another embodiment, the mutantincludes Ile at position 39 and Arg at position 40; Ile at position 39and Lys at position 40; Ile at position 39 and His at position 40; Valat position 39 and Arg at position 40; Val at position 39 and Lys atposition 40; Val at position 39 and His at position 40; Leu at position39 and Arg at position 40; Leu at position 39 and Lys at position 40;Leu at position 39 and His at position 40; Tyr at position 39 and His atposition 40; Phe at position 39 and His at position 40; Phe at position39 and Lys at position 40; Phe at position 39 and Arg at position 40;Trp at position 39 and Arg at position 40; Trp at position 39 and Lys atposition 40; Trp at position 39 and His at position 40; Ser at position39 and His at position 40; or Ser at position 39 and Thr at position 40.

In another non-limiting example, the YqhD mutant has a polypeptidesequence of SEQ ID NO:5 (FIG. 10G), or a fragment thereof, in which oneor more amino acid substitutions are present at positions 37, 38, 39,and/or 40. In one embodiment, the mutant includes one of the followingamino acids, independently, at position 37, 38, and 39: Gly, Ile, Tyr,Val, Leu, Phe, or any other conservative amino acid substitutiondescribed herein. In another embodiment, the mutant includes one of thefollowing amino acids at position 40: Ser, Pro, Arg, His, Lys, Trp, orany other conservative amino acid substitution described herein.

Other exemplary mutants include an IlvC mutant (e.g., a mutant having apolypeptide sequence with at least one amino acid substitution, ascompared to wild-type IlvC (e.g., such as SEQ ID NO:6 in FIG. 11A). Inone non-limiting embodiment, the IlvC mutant has a polypeptide sequenceof SEQ ID NO:7 (FIG. 11B), or a fragment thereof, in which one or moreamino acid substitutions are present at positions 71, 76, 78, 110, 146,185, and/or 433.

The mutants can have any useful characteristic provided during selectiveevolution. In one non-limiting instance, the mutant can have increasedreactivity with nicotinamide adenine dinucleotide (NADH), as compared toa wild-type reference protein. In another instance, the mutant can haveincreased reactivity NADH over nicotinamide adenine dinucleotidephosphate (NADPH), as compared to a wild-type reference protein. In yetanother instance, the mutant can have increased specificity for NADHover NADPH, as compared to a wild-type reference protein.

FIG. 3A shows a portion of an exemplary process including apre-treatment step 310, a fermentation step 320, adistillation/extraction step 330, and a lyophilization step 340. Each ofthese steps, in turn, can include one or more other sub-steps. Forinstance, pre-treatment 310 can include acid treatment 311 in order todegrade proteins and carbohydrates into soluble and/or hydrolyzedprotein and sugar; as well as enzyme treatment 312 in order to degradeproteins into amino acids. Each of these components (e.g., proteins,carbohydrates, sugars, amino acids, etc.) obtained from thepre-treatment step is considered a biocomponent. In some instances,pre-treatment 310 results in solubilization of useful biocomponents, aswell as separation of biomass solids.

Fermentation can include use of one or more organisms configured tofacilitate degradation (e.g., specific or non-specific degradation) ofone or more biocomponents. As can be seen, an exemplary fermentationstep 320 includes use of at least two organisms, in which a firstorganism 321 is useful for degradation of sugar into alcohol and inwhich a second organism 322 is useful for degradation of amino acid intoan alcohol (e.g., R^(A)OH, in which R^(A) is an optionally substitutedalkyl, such as an optionally substituted C₂₋₁₀ alkyl) and an amine(e.g., N⁺R¹R²R³R⁴ or NR¹R²R³, in which each of R¹, R², R³, and R⁴ is,independently, H or an optionally substituted alkyl). The fermentationstep 320 results in a fermentation product, which can include a mixtureof alcohols, amino acids, amines, and/or lipids.

After distillation/extraction 330, various fractions of the mixture canbe separated into different components, including a first fractionincluding mostly lipids and lipid products (e.g., a bioresidue); asecond fraction including mixed alcohols and, optionally, neutrallipids; and a third fraction including amines and/or amino acids. Thefirst fraction can be further processed (e.g., by way of liquefactionand/or pyrolysis) to produce a biocrude oil, which can be treated toform a biofuel. The second fraction can be further purified into, e.g.,bioethanol. The third fraction can be further processed to isolatehigh-value amino acids. In some embodiments, the pre-treatment andfermentation conditions herein can provide enhanced alcohol yield (see,e.g., FIG. 8), as well as enhanced amino acid degradation and enhancedfusel alcohol yield (FIG. 9).

The pre-treatment, distillation/extraction, and fermentation steps canbe conducted in any useful order. For instance, the fermentation stepcan be conducted prior to distillation/extraction, meaning that lipids,proteins, and carbohydrates, as well as derived components thereof, arepresent during fermentation.

Alternatively, the distillation/extraction step can be conducted priorto fermentation, meaning that the lipid fraction will be omitted fromthe fermentation step. FIG. 3B shows a portion of an exemplary processincluding a pre-treatment step 3003, a distillation/extraction step3005, and a fermentation step 3004. Pre-treatment 3003 can include thesub-steps of acid treatment 3013 in order to degrade proteins andcarbohydrates into soluble and/or hydrolyzed protein and sugar; as wellas enzyme treatment 3023 in order to degrade proteins into amino acids,thereby providing one or more biocomponents.

Next, a distillation/extraction 3005 step is conducted to provide afirst fraction including mostly lipids and lipid products (e.g., abioresidue) and a second fraction including soluble biocomponents. Thefirst fraction can be further processed (e.g., by way of liquefactionand/or pyrolysis) to produce a biocrude oil, which can be treated toform a biofuel. The second fraction can be fermented and furtherpurified into, e.g., bioethanol. As can be seen, an exemplaryfermentation step 3004 includes use of at least two organisms, in whicha first organism 3014 is useful for degradation of sugar into alcoholand in which a second organism 3024 is useful for degradation of aminoacid into alcohol and an amine (e.g., including ammonium).

The process can include a pre-treatment step that precedes eachfermentation step. FIG. 3C shows a portion of an exemplary processincluding a first pre-treatment step 3103, a distillation/extractionstep 3105, and a first fermentation step 3104. Pre-treatment 3103 caninclude acid treatment 3113 in order to degrade proteins andcarbohydrates into soluble and/or hydrolyzed protein and sugar, followedby fermentation 3104 with a first organism 3114 that is useful fordegradation of sugar into alcohol.

The process can be followed by a second pre-treatment step 3203 and asecond fermentation step 3214. Pre-treatment 3203 can include enzymetreatment 3213 in order to degrade proteins into amino acids, therebyproviding one or more biocomponent, followed by fermentation 3204 with asecond organism 3214 that is useful for degradation of amino acid intoalcohol and an amine (e.g., an ammonium).

Distillation/extraction steps can be conducted at any useful time duringthe process. FIG. 3D shows a portion of an exemplary process including afirst pre-treatment step 3503, a first fermentation step 3504, a secondpre-treatment step 3603, and a second fermentation step 3604.

Pre-treatment steps 3503,3603 can include acid treatment 3513 in orderto degrade proteins and carbohydrates into soluble and/or hydrolyzedprotein and sugar; or enzyme treatment 3613 in order to degrade proteinsinto amino acids. Fermentation steps 3504,3604 can include use of afirst organism 3514 that is useful for degradation of sugar into alcoholand a second organism 3614 that is useful for degradation of amino acidinto alcohol and an amine (e.g., an ammonium). Optionally, a firstdistillation/extraction step 3505 can be conducted after the firstfermentation step 3504, thereby isolating bioethanol and removing thispotentially inhibitory product from the fermentation product. In anotherexample, a second distillation/extraction step 3605 can be conductedafter the second fermentation step 3604, thereby isolating mixedalcohols from the fermentation product. In yet another example, afurther separation step (e.g., a lyophilization step 3606) can beemployed to isolate amino acids from the fermentation product.

Distillation/Extraction

The alcohol fermentation products, lipids, and amino acids from thebiomass can be captured by distillation and solvent co-extraction.Retaining the lipids through the protein fermentation has beendemonstrated to increase yield by reducing product inhibition by phasesegregation into lipid microparticles, which can be extracted bylipophilic solvents, such as hexane and ethyl acetate, avoiding highenergy fractional distillation of the more than C₂ alcohol (e.g., C₂₋₁₀alcohol) and lipid products.

Any useful distillation and extraction techniques can be employed,including flash extraction, ionic liquid extraction, etc., to isolateone or more biocrude oil, aqueous phases, aqueous co-products,nutrients, etc.

Thermal Conversion, Liquefaction or Pyrolysis

High-temperature treatment (e.g., liquefaction or pyrolysis) can be usedto separate or convert particular components of the biomass solids,bioresidue, etc. Exemplary thermal conversion conditions include use ofcatalysts, use of hydrogen (e.g., in hydrotreatment), use of water(e.g., in liquefaction, including sub-critical or super-critical water),use of aerobic conditions, use of anaerobic conditions (e.g., inpyrolysis), use of high pressure (e.g., of from about 2,000 psi to about3,000 psi), and/or use of high temperatures (e.g., of from about 200° C.to about 800° C.) to decompose the bioresidue into small molecules,which in turn can react and repolymerize to form oily compounds within abiocrude oil.

In one instance, the thermal conversion condition includes liquefaction,which is generally conducted in the presence of water. By using hightemperature and/or high pressure conditions, water becomes a reactivecompound that converts the bioresidue into a biocrude oil. Exemplaryliquefaction conditions include a wet biomass (e.g., more about 70%moisture), a temperature of from about 200° C. to about 500° C., and apressure of from about 4 to about 25 MPa.

In another instance, the thermal conversion condition includespyrolysis, which is generally conducted in the absence of water and inanaerobic conditions. Exemplary pyrolysis conditions include a drybiomass (e.g., less than about 5% moisture), a temperature of from about200° C. to about 750° C., and a pressure of from about 0.1 to about 0.5MPa.

Exemplary thermal conversion conditions are described in Ma F et al.,“Biodiesel production: a review,” Bioresourc. Technol. 1999; 70:1-15;Naik S N et al., “Production of first and second generation biofuels: acomprehensive review,” Renew. Sustain. Energy Rev. 2010; 14:578-97;Raheem A et al., “Thermochemical conversion of microalgal biomass forbiofuel production,” Renew. Sustain. Energy Rev. 2015; 49:990-9; RingerM et al., “Large-scale pyrolysis oil production: a technology assessmentand economic analysis,” National Renewable Energy Laboratory TechnicalReport NREL/TP-510-37779, November 2006, 93 pp.; and Schneider R C S etal., “Potential production of biofuel from microalgae biomass producedin wastewater,” in Biodiesel—Feedstocks, Production and Applications,Prof Zhen Fang (ed.), InTech, 2012, 22 pp., each of which isincorporated herein by reference in its entirety.

Any of the liquefaction steps herein can be replaced by any otherthermal conversion step (e.g., pyrolysis) in which high temperatureconditions are employed to thermally degrade a bioresidue.

Hydrotreatment

Hydrotreatment is generally used to convert compositions into usefulintermediate products or end-use products. Such hydrotreatment generallyincludes use of high temperatures to institute any useful chemicalchange, e.g., to break apart triglycerides; to form low molecular weightcarbon species, such as optionally substituted alkanes, cycloalkanes, oraryls; to saturate carbon chains with hydrogen; to denitrogenatespecies; and/or to deoxygenate species to form alkanes, such asn-alkanes. For instance, hydrotreatment can be used to upgrade biocrudeoil into biofuels, biochar, or ash; as well as to convert aqueousco-products into biogas. Biocrude oil produced from thepost-fermentation residuals by HTL is indicated to have ˜50% reductionin nitrogen (primary and secondary amines), thus making it acceptablefor hydrotreatment using the existing petrochemical infrastructure.

Hydrotreatment can include isomerization, hydrocracking, distillation,hydrodeoxygenation, catalytic processing (e.g., such as use of one ormore catalysts to remove nitrogen, oxygen, and/or sulfur from thebiocrude oil under any useful condition, such as a pressure of fromabout 5 MPa to about 15 MPa and a temperature of from about 200° C. toabout 450° C.), liquefaction (e.g., such as hydrothermal liquefaction(HTL) or catalytic liquefaction of a biocrude oil into a biofuel or abiofuel intermediate by use of an operating temperature of from about100° C. to about 500° C.), transesterification (e.g., treatment ofbiocrude oil with an alcohol and an optional catalyst to produce methylester biodiesel), and/or catalytic hydrothermal gasification (CHG)(e.g., of an aqueous co-product into biogas).

The hydrotreatment process can employ any useful catalyst (e.g., a metalcatalyst, such a copper-based catalyst (e.g., CuCr, CuO), a nickel-basedcatalyst (e.g., NiMo), a ruthenium-based catalyst, a palladium-basedcatalyst (e.g., Pd/C), a platinum-based catalyst, a rhenium-basedcatalyst, or a cobalt-based catalyst (e.g., CoMo)) in the presence ofany carrier (e.g., a zeolite, an alumina, etc.); any useful reagent,such as hydrogen (e.g., H₂) or water (e.g., supercritical water); anyuseful pressure, e.g., such as from about 3 MPa to about 30 MPa (e.g.,from about 5 MPa to about 20 MPa); and/or any useful temperature, e.g.,such as from about 100° C. to about 500° C. (e.g., from about 250° C. toabout 350° C.). Further exemplary hydrotreatment conditions aredescribed in Ma F et al., “Biodiesel production: a review,” Bioresourc.Technol. 1999; 70:1-15; Tran N H et al., “Catalytic upgrading ofbiorefinery oil from micro-algae,” Fuels 2010; 89:265-74; and WildschutJ et al., “Catalyst studies on the hydrotreatment of fast pyrolysisoil,” Appl. Catalysis B 2010; 99:298-306, each of which is incorporatedherein by reference in its entirety.

Exemplary biofuels formed by hydrotreatment include naphtha, biodiesel(e.g., including one or more unsaturated fatty acids or fatty acidesters, such as of from about 10% to about 35% of a long chain fattyacid having a C₁₃-C₂₁ tail, such as a palmitic fatty acid (C₁₆ tail),linoleic fatty acid (C₁₈ tail), oleic fatty acid (C₁₈ tail), and/orstearic fatty acid (C₁₈ tail)), green diesel, renewable aviation fuel,hydrocarbons (e.g., light hydrocarbons), alcohol (e.g., ethanol;propanol, such as 1-propanol; butanol, such as n-butanol, isobutanol,2-butanol, 3-butanol, 2-methyl-1-butanol, 3-methyl-1-butanol, etc.),and/or a biogas (e.g., hydrogen or methane). Other products formed byhydrotreatment include solid residuals (e.g., biochar and ash), aqueousco-products (e.g., ketoacids, amines, nutrients, etc.), as well as otheruseful co-products (e.g., animal feed, fertilizer, glycerine,biopolymers, etc.).

Phase Separation

Phase separation steps can be employed to separate components of aliquefied mixture, fermentation broth, aqueous fraction, a non-aqueousfraction, alcohol fraction, etc. Such steps include any that separateliquid from solid phases, as well as separate two or more phases thatcan be differentiated based on solubility, miscibility, etc. (e.g., asthose present in non-aqueous phases, aqueous phases, lipophilic phases,etc.) in any useful solvent (e.g., an organic solvent, an aqueoussolvent, water, buffer, etc.). Phase separation techniques include flashseparation (e.g., separation of liquefied mixture into biocrude oil,solid residuals, aqueous phase, and/or aqueous co-products), acidabsorption (e.g., absorption of acid in a matrix to provide recoverednutrients and water for recycled use), filtration, distillation, solventextraction, ion liquid extraction, etc. The resultant products andco-products can include one or more intermediate products that canoptionally be processed to form useful end-use products.

EXAMPLES Example 1: Biochemical Upgrading of Dried Distillers Grains

Dried distillers grains are a high-protein biomass that is recalcitrantto further processing. The methods described herein provide a process toupgrade this biomass into useful intermediates and by-products. In oneembodiment, the method includes an integrated sugar and proteinfermentation process, with pre-treatment steps to facilitatefermentation. The method can include use of a dilute acid (e.g., use of2-10% H₂SO₄ at a temperature of from about 90° C. to 145° C. for anyuseful incubation period, such as about 30 minutes to 6 hours) prior touse of a sugar fermentation strain (e.g., E. coli KO11) to convertsugars into ethanol. The method can also include use of an enzyme (e.g.,about 0.5 g/L to 2 g/L of a protease or protease cocktail at atemperature of from about 37° C. to 55° C. for any useful incubationperiod, such as from about 12 to 48 hours) prior to use of a proteinfermentation strain (e.g., E. coli YH83 with one or more additionalmutated variations) to convert amino acids to alcohols (e.g., more thanC₂ alcohols, such as C₃₋₁₀ alcohols) and amines (e.g., NH₄).

Any useful biomass can be processed. In particular, high-protein biomasscan be particularly beneficial. Exemplary biomass include drieddistillers grains with solubles (DDGS), soy products (e.g., soy meal),yeast products (e.g., yeast extract), whey, algae (e.g., microalgae,macroalgae, diatoms, green algae, yellow algae, phytoplankton, plankton,protists, haptophytes, chlorophyta, and/or cyanobacteria), etc. FIG.4A-4B provides the potential conversion yield of various biomass, aswell as the potential yield of unutilized high value amino acids. As aninitial step, processing methods in this Example were employed with DDGSsamples.

Fermentation strains were developed and identified. As seen in FIG. 5,genetic engineering of E. coli resulted in organisms with high activityunder anaerobic or microaerobic conditions. Our approach focused on, inpart, altering the cofactor specificity of two enzymes in the pathwaythat provides isobutanol. In particular, two enzymes in the keto-acidpathway were modified: ketol-acid reductoisomerase IlvC and alcoholdehydrogenase YqhD. Generally, the wild-type strain employs a NADPHcofactor having a 2′-phosphate group. Modifications for the mutants wereoptimized to provide increased activity in the presence of a non-nativeNADH cofactor, as compared to the wild-type strain.

Mutant strains included AY1 (replacing IlvC with mutant A combined withreplacing YqhD with mutant Y1), AY2 (replacing IlvC with mutant Acombined with replacing YqhD with mutant Y2), AY3 (replacing IlvC withmutant A combined with replacing YqhD with mutant Y3), AY5 (replacingIlvC with mutant A combined with replacing YqhD with mutant Y5), VY2(replacing IlvC with mutant V combined with replacing YqhD with mutantY2), VY3 (replacing IlvC with mutant V combined with replacing YqhD withmutant Y3), VY5 (replacing IlvC with mutant V combined with replacingYqhD with mutant Y5), IA (replacing IlvC with mutant A), and IV(replacing IlvC with mutant V). Additional details for these mutantstrains are described herein. In particular, five new E. coli strainsshowed increased conversion yield, as compared to the wild-type YH83strain.

FIG. 6 shows an exemplary process flow for use with modifiedfermentation stains. This exemplary process can be optimized by varyingthe dilute acid pre-treatment conditions, by employing enzymaticpre-treatment at particular points of the process, and by separating thetwo fermentation steps, in which each step uses a different strain (see,e.g., FIG. 7).

Dilute acid pre-treatment and fermentation achieved enhancedbioconversion of carbohydrates (e.g., sugars) into ethanol. As seen inFIG. 8, dilute acid hydrolysis pre-treatment resulted in more than 90%hydrolysis of various carbohydrates, including glucose, xylose, andarabinose. After treatment with 4% hot acid for 72 hours, theconcentrations of these three representative sugars were decreased, andthe concentration of ethanol increased at a theoretical conversion yieldof about 60.7%. Improved xylose degradation can be promoted in anyuseful manner, e.g., by increasing the incubation temperature,increasing the concentration of the acid during pre-treatment, includinga pre-treatment step with basic conditions (e.g., in the presence ofNaOH or KOH), and/or by including one or more enzymes to cleave xylose,such as an isomerase, a reductase, etc.

Enzymatic pre-treatment and fermentation achieved enhanced bioconversionof proteins into fusel alcohol (e.g., more than C₂ alcohols, such asisobutanol, isopentanol, and/or phenylethanol) and amines. Enzymaticpre-treatment combined with dilute acid pre-treatment resulted in morethan 90% hydrolysis of various carbohydrates. Furthermore, as seen inFIG. 9, after treatment for 72 hours, the concentration of amino acidswas decreased, and the concentration of various fusel alcohols increasedat a theoretical conversion yield of about 40.8%. Improved resistance toproduct inhibition can be promoted in any useful manner, e.g., byemploying one or more separation or extraction steps; or by employingone or more lipids to promote vesicle formation.

Example 2: Cofactor Engineering to Improve the Fusel Alcohol Yield

Algal protein, as well as other high-protein feedstock, can be feasiblyconverted into fusel butanol with an engineered E. coli strain. Inparticular, algal protein has been used for producing fuel compounds,but the titer of fusel butanol is generally relatively low. One possiblereason is cofactor imbalance during the algal protein fermentation.

To resolve this problem, a direct evolution approach was applied toswitch the cofactor specificity of two enzymes (IlvC and YqhD) in theisobutanol pathway. These two enzymes rely on native cofactor NADPH inthis pathway. Cofactor switching can allow for reactivity in thepresence of a non-native cofactor (NADH), even if the native cofactor(NADPH) is lacking (e.g., such as in microaerobic or anaerobicconditions). Through high throughput screening, more than 20 YqhDmutants showed the activity with NADH.

Five YqhD mutants were selected and then combined with one of two IlvCmutants to reengineer the production strain. Upon combining thebeneficial mutations of IlvC and YqhD, the engineered E. coli strain AY3provided an optimized performance, in which fusel butanol yieldincreased by about 60%, as compared to wild-type E. coli, underanaerobic fermentation with an amino acid mixture. When applied to algalprotein hydrolysates, the engineered AY3 strain produced from about 38%to 100% more fusel butanol in the fermentation broth, as compared towild-type. This study provides a promising approach to improvebioconversion of algal protein into fusel butanol (e.g., as advancedfuel compounds) and amino acids (e.g., for further processing asnutrients or chemical intermediates). Additional details for this studyare provided in Example 3. The following materials and methods wereemployed for this study.

Strains and Plasmids:

The mutant E. coli strain YH83 (BW25113/F′ [traD36, proAB+,lacI^(q)ZΔM15]ΔglnAΔgdhAΔluxSΔlsrA) containing plasmids pYX68, pYX90,and pYX97 was generously provided by Professor James C Liao fromUniversity of California, Los Angeles (UCLA) (see, e.g., Huo Y X et al.,Nat. Biotechnol. 2011; 29(4):346-51). The strain was engineered forbioconversion of protein hydrolysates into isobutanol. Plasmids pYX90and pYX97 contained IlvC and YqhD, which use NADPH as the cofactor.Plasmid pBbE1a and the E. coli strain DH1 were used for the expressionand screening of mutant libraries of enzyme YqhD, as well as for thecreation of IlvC mutants.

Selection of Cofactor Binding Sites:

The amino acids for mutation in YqhD were selected by inspecting thecofactor NADPH binding site. Autodock 4 was used to investigate thecofactor-enzyme interaction. The protein X-ray structure of E. coli K-12YqhD (Entry No. 1OJ7) containing cofactor NADPH was extracted from RCSBProtein Data Bank.

Mutant Library Construction, Expression, and High-Throughput Screening:

Plasmid pBbE1a was generously provided by Dr. Taek Soon Lee from JointBioEnergy Institute. Genes IlvC and YqhD were amplified from plasmids(pYX90 and pYX97), and then sub-cloned into vector pBbE1a underrestriction cutting sites (EcoRI and BamHI) to achieve vectorspBbE1a-IlvC and pBbE1a-YqhD, respectively. Saturation mutagenesis wasapplied to create a recombinant mutant library of enzyme YqhD, followingthe description in the previous study (see, e.g., Wu W et al.,“Site-saturation mutagenesis of formate dehydrogenase from Candidabodinii creating effective NADP⁺-dependent FDH enzymes,” J. Molec.Catal. B 2009; 61(3-4):157-61). For the recombinant library of YqhD,primers with degenerate codons were used to create mutations at theselected amino acid sites. High fidelity DNA polymerase fusion Q5 (NewEngland BioLabs, Inc. (NEB), Ipswich, Mass.) was used to generate thelibrary and to express library members in E. coli DH1. Strainscontaining YqhD mutants were diluted properly and spread ontoLuria-Bertani (LB) plates supplemented with ampicillin (100 μg/mL) forthe following library screening.

According to the previous study (see, e.g., Bastian S et al., Metab.Eng. 2011; 13(3):345-52), the two mutant IlvCs (A71S, R76D, S78DQ110V/Q110A) switched the cofactor specificity from NADPH to NADH withthe relatively high activity with NADH. Site mutagenesis (pointmutation) was used to create two mutants of enzyme IlvC at the fourtarget amino sites mentioned above. An iterative strategy was used tocreate all four sites of mutations. High fidelity DNA polymerase fusionQ5 was again used to create point mutations of IlvC in the vectorpBbE1a-IlvC, as described before (see, e.g., Wu W et al., J. Molec.Catal. B 2009; 61(3-4):157-61). Mutations were confirmed through DNAsequencing. All the primers used herein are listed in Table 1, below.

TABLE 1  Primers and mutants for YqhD and IlvC SEQ ID Name Sequence NO:Notes YqhD-pBbE1a-F 5-CTC AGC  GAA TTC  ATG AAC AAC TTT AAT CTG CAC 10Clone YqhD ACC CCA AC-3 into pBbE1a YqhD-pBbEla-R 5-TGACCT GGATCCTTA GCG GGC GGC TTC GTA TAT AC-3 11 IlvC-pBbE1a-F 5-CTC AGC  GAA TTC ATG GCT AAC TAC TTC AAT ACA 12 Clone IlvC CTG AAT CTG C-3 into pBbE1aIlvC-pBbE1a-R 5-TGACCT GGATCC  TTA ACC CGC AAC AGC AAT ACG TTT 13 C-3YqhD-S40-F 5-GTATTGATTACCTACGGCGGC GGC NNN GTG AAA AAA 14 Create mutantACC GGC GTT CTC-3 library S40 YqhdS40-R5-GAG AAC GCC GGT TTT TTT CAC NNN GCC GCC GCC 15 GTA GGT AAT CAA TAC-3YqhD-G39S40-F 5-GTATTGATTACCTACGGCGGC NNN NNN GTG AAA AAA 16Create mutant ACC GGC GTT CTC-3 library Yqhd-G39S40-R5-GAG AAC GCC GGT TTT TTT CAC NNN NNN GCC GCC 17 G39S40GTA GGT AAT CAA TAC-3 YqhD-S40P-F5-GTATTGATTACCTACGGCGGC CCG GTG AAA AAA ACC 18 Mutant Y1 GGC GTT CTC-3(S40P) Yqhd-S40P-R 5-GAG AAC GCC GGT TTT TTT CAC CGG GCC GCC GTA 19GGT AAT CAA TAC-3 YqhD-S40R-F5-GTATTGATTACCTACGGCGGC CGT GTG AAA AAA ACC 20 Mutant Y2 GGC GTT CTC-3(S40R) Yqhd-S40R-R 5-GAG AAC GCC GGT TTT TTT CAC CGT GCC GCC GTA 21GGT AAT CAA TAC-3 YqhD- 5-GTATTGATTACCTACGGCGGC ATCCGT GTG AAA AAA 22Mutant Y3 G39I/S40R-F ACC GGC GTT CTC-3 (G39I/S40R) YqhD-5-GAG AAC GCC GGT TTT TTT CAC ACG GAT GCC GCC 23 G39I/S40R-RGTA GGT AAT CAA TAC-3 YqhD- 5-GTATTGATTACCTACGGCGGC TATCAT GTG AAA AAA24 Mutant Y5 G39Y/S40H-F ACC GGC GTT CTC-3 (G39Y/S40H) Yqhd-5-GAG AAC GCC GGT TTT TTT CAC ATG ATA GCC GCC 25 G39Y/S40H-RGTA GGT AAT CAA TAC-3 IlvCA71SR76DS 5-CGT AAA GAA 

CG ATT GCC GAG AAG G

 GCG 

26 78D-F TGG-3 IlvCA71SR76DS5-CCA ATC CGC ATC CTT CTC GGC AAT CGA TTC TTT 27 78D-R ACG-3 ilvCQ110A-F5-CGG ACA AGG CGC ACT CTG ATG TAG-3 28 Mutant A ilvCQ110A-R5-CTA CAT CAG AGT GCG CCT TGT CCG-3 29 (A71S/R76/ S78D/Q110) ilvCQ110V-F5-CGG ACA AGG TGC ACT CTG ATG TAG-3 30 Mutant V ilvCQ110V-R5-CTA CAT CAG AGT GCA CCT TGT CCG-3 31 (A71S/R76D/ S78D/Q110)ILVC-Pyx90- 5-GAA AGC TCT CTA GGT CGA CGA GGA ATC ACC ATG 32Replace IlvC Gib-F1 GCT AAC TAC TTC AAT ACA CTG AAT CTG-3 with mutantILVC-Pyx90- 5-GTA CTT AGG CAT GGT ATA TCT CCT TCC GGG TTA 33 A or VGib-R1 ACC CGC AAC AGC AAT ACG TTT CAT ATC-3 ILVD-AvTA-5-GAT ATG AAA CGT ATT GCT GTT GCG GGT TAA CCC 34 pYX90-Gib-F2GGA AGG AGA TAT ACC ATG CCT AAG TAC-3 ILVD-AvTA-5-GGA TTT GTC CTA CTC AGG AGA GCG TTC ACC GAC 35 pYX90-Gib-R2AAA CAA CAG ATA AAA CGA AAG GCC CAG-3 Spec-alsS-5-CTG GGC CTT TCG TTT TAT CTG TTG TTT GTC GGT GAA 36 pYX90-Gib-F3CGC TCT CCT GAG TAG GAC AAA TCC-3 Spec-alsS-5-CAG ATT CAG TGT ATT GAA GTA GTT AGC CAT GGT 37 pYX90-Gib-R3GAT TCC TCG TCG ACC TAG AGA GCT TTC-3 YqhD-Pyx97-5-GGA GAA AGG TCA CAT GAA CAA CTT TAA TCT GCA 38 Replace YqhD Gib-F1CAC CCC AAC CCG CAT TC-3 with mutant YqhD-Pyx97-5-CTC TAG CAC GCG TAC CAT GGG ATC CTT AGC GGG 39 Y1, Y2, Y3, or Gib-R1CGG CTT CGT ATA TAC-3 Y5 ColE-Amp-5-GTA TAT ACG AAG CCG CCC GCT AAG GAT CCC ATG 40 pYX97-Gib-F2GTA CGC GTG CTA GAG-3 ColE-Amp-5-CAT GAT AAT AAT GGT TTC TTA GAC GTC AGG TGG 41 pYX97-Gib-R2CAC TTT TCG GGG AAA TGT GCG CGG AAC-3 LeuDH-KivD-5-GTT CCG CGC ACA TTT CCC CGA AAA GTG CCA CCT 42 pYX97-F3GAC GTC TAA GAA ACC ATT ATT ATC ATG-3 LeuDH-KivD-5-GAA TGC GGG TTG GGG TGT GCA GAT TAA AGT TGT 43 pYX97-R3TCA TGT GAC CTT TCT CC-3

Single colonies of YqhD mutant and wild-type were cultured into 96-wellplates. Each well contained 200 μl of LB medium with correspondingantibiotics. Cultures were incubated at 300 rpm and at 37° C. overnight(16 hours) and induced by 1.0 mM isopropyl β-d-1-thiogalactopyranoside(IPTG) for another 24 hours at 250 rpm, 30° C. in a humidified shaker.Cells were harvested by centrifugation (3000 rpm, 4° C., 15 min.) andstored at −20° C. before conducting assays. For high-throughputscreening assays, E. coli cells were lysed with 200 μl of 50 mM MOPS (pH7.0) containing 1 mg/ml of lysozyme (Sigma-Aldrich Corp., St. Louis,Mo.) and 20 U/ml of DNase (NEB) at 4° C. for 6 hours under gentleshaking. Lysed cells were spun down, and 100 μl of the cell free extractwas transferred into another 96 well plate. YqhD and its mutant activityassay buffer contained 50 μl of 0.25 mM NADH, 10 μl of isobutyraldehyde,and 40 μl of MOPS (pH 7.0). Consumption of NADH was monitored at 340 nmin a plate reader (Molecular Devices, LLC, Sunnyvale, Calif.).

Plasmids and Strain Construction for Anaerobic Bioconversion of AlgalProtein Hydrolysates:

Positive hits with high activity with NADH were selected to replace thewild-type YqhD gene in plasmid pYX97. Two mutant genes of IlvC wereselected to replace the wild-type IlvC gene in plasmid pYX90. A Gibsonassembly was applied to replace wild-type YqhD and IlvC with thecorresponding mutant genes. Plasmids pYX97 and pYX90 with mutant genes,as well as pYX68 were co-transformed into strain YH40 for thebioconversion of algal protein hydrolysates into fusel butanol. All theprimers used herein are listed in Table 1, above.

Addition of NADPH into Fermentation Media:

Wild-type strain YH83 was cultured in 20 ml of LB media with 100 μg/mlampicillin, 34 μg/ml chloramphenicol, and 25 μg/ml spectinomycinovernight. Then, 5 ml of culture was transferred into 150 ml of 1×M9medium (see, e.g., Huo Y X et al., Nat. Biotechnol. 2011; 29(4):346-51;and Wu W, “Fuel ethanol production using novel carbon sources andfermentation medium optimization with response surface methodology,”Int. J. Agri. Biol. Eng. 2013; 6(2):42-53) (in 160 ml serum bottle)containing 20 g/L of an amino acid mixture, 2 g/L of LB, and 150 μMNADPH with corresponding aforementioned antibiotics in a rotary shakerat 220 rpm, 37° C. The culture was induced by 1 mM IPTG at 37° C. whenthe OD reached 0.6 for the production of fusel butanol. Samples weretested at regular time intervals to determine the concentration of fuselbutanol in each sample. Each run was performed in biological duplicate.

Investigation of the Fusel Butanol Yields with an Amino Acid Mixture:

Engineered strains of YH83 containing various combinations of mutantYqhD and IlvC were cultured in 20 ml of LB media with correspondingaforementioned antibiotics, overnight. Then, 3 ml of culture wastransferred into 30 ml of 1×M9 medium containing 20 g/L of an amino acidmixture (Sigma-Aldrich, Corp.), 5 g/L of LB, and antibiotics.Fermentation was performed as described above. Each run was performed inbiological duplicate. Strains containing the details of the mutants arelisted in Table 1, above.

Bioconversion of Algal Protein Hydrolysates into Fusel Butanol:

ATP algae biomass samples were pretreated with diluted acid, accordingto the protocol from the National Renewable Energy Laboratories(referenced hereinafter as “ATP3”) or according to the protocoldescribed previously (see, e.g., Garcia-Moscoso J L et al., “Kinetics ofpeptides and arginine production from microalgae (Scenedesmus sp.) byflash hydrolysis,” Ind. Eng. Chem. Res. 2015; 54(7):2048-58) through athermal flash hydrolysis (referenced hereinafter as “ODU”). Hydrolyzedalgal carbohydrate was converted into ethanol through alcoholicfermentation using an ethanogenic strain, E. coli KO11. The cell masswas removed through centrifugation (6,000 rpm, 4° C., 10 min.) at theend of KO11 fermentation. The supernatant containing ethanol and algalprotein was air-bubbled at room temperature for 10 minutes to removeethanol. Then, the resultant supernatant was concentrated and digestedwith 2 mg/mL Pronase® (Promega Corp., Madison, Wis.) following themanufacturer's protocol. The protease-digested, algal proteinhydrolysate was sterilized through a 0.45 μm PTFE membrane and used asthe fermentation media for fusel butanol production. This hydrolysatewas incubated with mutant strain AY3 in the presence of the amino acidmixture. Samples were tested at regular intervals with GC-MS analysis.Each run was performed in biological duplicate.

Analytic Determination of the Presence of Fusel Butanol and Amino Acid:

Concentrations of amino acids were analyzed using an amino acid analyzer(Hitachi Ltd., Tokyo, Japan) at the genome center of University ofCalifornia, Davis, following their protocol. Fusel butanol was extractedusing ethyl acetate at a ratio of 1:1 (ethyl acetate: fermentationbroth), with 2-methyl-pentanol as an internal reference. The mixture wasvortex at 1,200 rpm for 20 min. and centrifuged at 14,000 rpm, 5 min.The ethyl acetate layer was collected for further GC-MS analysis. Two μlof sample was inserted into the injection port (220° C.) of an Agilent7890A Gas Chromatograph containing a 30 m×0.25 mm i.d. DB wax capillarycolumn with a film thickness of 0.25 μm. The column was temperatureprogrammed as follows: 40° C. for 4 min., increasing to 65° C. at 10°C./min. and holding for 10 min., then increasing to 120° C. at 10°C./min. and holding for 2 min., and then increasing to 220° C. at 20°C./min and holding for 5 min. The carrier gas was ultra-high purityhelium at a constant flow rate of 1.8 ml/min. The initial column headpressure was 16.188 psi with a split ratio of 10. The gas chromatographwas coupled to a quadrupole mass selective detector (MSD), Agilent5975C. The MSD parameters included EI at 70 eV, mass range at 10-650 Da,and scan speed at 2 scans/sec. Spectral components were searched againstthe NIST 2015 mass spectral library. Serial of dilutions of isobutanoland 2-methyl-butanol in ethyl acetate were analyzed to determine astandard curve. Concentrations of fusel butanol were calculated byreferring samples to the standard curve.

Example 3: Cofactor Engineering of Ketol-Acid Reductoisomerase (IlvC)and Alcohol Dehydrogenase (YqhD)

Increasing concerns about diminishing fossil fuels and globalenvironmental problems have attracted interest in sustainable biofuelsobtained from renewable resources (see, e.g., Peralta-Yahya P P et al.,“Microbial engineering for the production of advanced biofuels,” Nature2012; 488(7411):320-8; and Keasling D, “Sustainable production ofadvanced biofuels,” 241st ACS National Meeting & Exposition, held on27-31 Mar. 2011 in Anaheim, Calif., Abstract 202). Algae-based biofuelis considered to be one sustainable alternative biofuel due to severalbenefits, including simplified pretreatment as compared tolignocellulosic biomass, higher biomass yields as compared to plants,possible cultivation on nonarable land, and possible reclamation ofwaste water (see, e.g., Razeghifard R, “Algal biofuels,” Photosynth.Res. 2013; 117(1-3):207-19; and Luque R, “Algal biofuels: the eternalpromise?,” Energy Environ. Sci. 2010; 3:254-7). So far, algae biomasshave been converted to versatile biofuel chemicals, such as bioethanol,biohydrogen, biogas, crude oil, and biodiesel (see, e.g., Li K et al.,“An overview of algae bioethanol production,” Int. J. Energy Res. 2014;38(8):965-77; Melis A et al., “Hydrogen production: green algae as asource of energy,” Plant Physiol. 2001; 127(3):740-8; Hernández D etal., “Biofuels from microalgae: lipid extraction and methane productionfrom the residual biomass in a biorefinery approach,” Bioresour.Technol. 2014; 170:370-8; López Barreiro D et al., “Assessing microalgaebiorefinery routes for the production of biofuels via hydrothermalliquefaction,” Bioresour. Technol. 2014; 174:256-65; Sharma K K et al.,“High lipid induction in microalgae for biodiesel production,” Energies2012; 5(5):1532-53; and Scott S A et al., “Biodiesel from algae:challenges and prospects,” Curr. Opin. Biotechnol. 2010; 21(3):277-86).

Current state-of-the-art algal biofuels have primarily focused onproducing biodiesel by boosting algal lipid yield under nutrient stressconditions. This strategy ignores another major component of algae:proteins. Under conditions that support robust algae growth, algalcarbohydrate and proteins are two of the major components of biomass,including up to ˜80% of the ash-free dry weight (AFDW) of microalgaebiomass, in which up to 60% can be proteins (see, e.g., Luque R, EnergyEnviron. Sci. 2010; 3:254-7; Becker E W, “Microalgae: biotechnology andmicrobiology,” Cambridge University Press, Cambridge, U.K., 1994 (293pp.); and Singh J et al., “Commercialization potential of microalgae forbiofuels production,” Renew. Sustain. Energy Rev. 2010; 14(9):2596-610).

Recently, engineered E. coli strains have been employed to convert algalprotein into fusel butanol. Modified strains can be selected to exhibitdeamination of protein hydrolysates to C4 and C5 alcohols at 56% of thetheoretical yield (see, e.g., Huo Y X et al., “Conversion of proteinsinto biofuels by engineering nitrogen flux,” Nat. Biotechnol. 2011;29(4):346-51). By combining the Ehrlich pathway with three exogenoustransamination and deamination cycles, the engineered E. coli strainproduced up to 0.183 g of fusel butanol/g of amino acids under aerobicor microaerobic fermentation conditions (see, e.g., Huo Y X et al., Nat.Biotechnol. 2011; 29(4):346-51). In some instances, anaerobic conditionscan be preferred for large scale fermentation due to lower operatingcosts and higher theoretical yield.

In the Ehrlich pathway for isobutanol production, two enzymes usenicotinamide adenine dinucleotide phosphate (NADPH) as a cofactor:ketol-acid reductoisomerase (IlvC) and alcohol dehydrogenase (YqhD).Thus, bioconversion of protein hydrolysates requires at least tworeducing equivalents of NADPH to convert glucose to isobutanol (see,e.g., Atsumi S et al., “Non-fermentative pathways for synthesis ofbranched-chain higher alcohols as biofuels,” Nature 2008;451(7174):86-9). Under anaerobic fermentation, glycolysis can onlyproduce nicotinamide adenine dinucleotide (NADH) as an availablereducing equivalent, while the pentose phosphate pathway (PPP) and thetricarboxylic acid (TCA) cycle are not functional due to the lack ofoxygen. This may result in a cofactor imbalance during anaerobicfermentation or oxygen limited fermentation conditions (e.g.,microaerobic conditions). Thus, although anaerobic or microaerobicfermentation is preferred to minimize processing costs and to increasetheoretical yields, these very fermentation conditions can result in aninhibitory cofactor imbalance that can limit alcohol production.

NADPH limitation can result in cofactor imbalance, as reportedpreviously for isobutanol production from glucose (see, e.g., Shi A etal., “Activating transhydrogenase and NAD kinase in combination forimproving isobutanol production,” Metab. Eng. 2013; 16:1-10; and BastianS et al., “Engineered ketol-acid reductoisomerase and alcoholdehydrogenase enable anaerobic 2-methylpropan-1-ol production attheoretical yield in Escherichia coli,” Metab. Eng. 2011; 13(3):345-52).Therefore, we hypothesized that fusel butanol yield can be improvedthrough resolving the cofactor imbalance present in anaerobicfermentation of algal protein.

To achieve this, we first tested our hypothesis that lack of NADPHaffects fusel alcohol production. Thus, we performed experiments byadding NADPH in the fermentation media, and observing the effect ofNADPH on alcohol yield. Then, we designed two isobutanol biosynthesispathway enzymes (IlvC and YqhD) to switch cofactor specificity fromNADPH to NADH through directed evolution. Upon combining the beneficialmutations of two enzymes in the isobutanol biosynthesis pathway, theresultant engineered E. coli strain improved fusel butanol yield byabout 60%, as compared to wild-type, under anaerobic fermentationconditions with an amino acid mixture as the feedstock. When applied toalgal protein hydrolysates, the mutant strain with best performanceproduced 38% to 100% more fusel butanol, as compared to wild-type.

Engineering the Cofactor Specificity of E. coli IlvC and YqhD to Switchto NADH:

The x-ray crystal structure of YqhD had been reported previously (see,e.g., Sulzenbacher G et al., “Crystal structure of E. coli alcoholdehydrogenase YqhD: evidence of a covalently modified NADP coenzyme,” J.Mol. Biol. 2004; 342(2):489-502). This structure contained cofactorNADP⁺ as a ligand. The protein possesses a GGGS (residues 37-40) motif,which binds the 2′-phosphate groups of NADP through hydrogen bonds, asshown in FIG. 10A (phosphorous and oxygen atoms of the 2′-phosphate isindicated by P, O, and dashed lines). These hydrogen bonds provide apreference for binding NADPH over NADH, making the motif GGGS a majorcofactor binding site. Therefore, two amino acids (Gly39Ser40) werechosen to identify mutations that would confer cofactor switching fromNADPH to NADH through site-saturation mutagenesis.

Two mutant libraries (G39S40 and S40) were generated and screened forNADH activity using a cell free extract. More than 20 positive mutantsshowed various activities with cofactor NADH. Five mutants showed 60-80times higher activity with NADH (as shown in FIG. 10B), as compared towild-type YqhD (FIG. 10C). The five mutants were selected to replacewild-type YqhD in plasmid pYX97, including two single mutations of S40(Y1, Y2) (see, e.g., FIG. 10D-10E) and three double mutations of G39S40(Y3, Y4, Y5) (see, e.g., FIG. 10F).

E. coli IlvC has been engineered to switch cofactor from NADPH to NADHfor isobutanol production under anaerobic fermentation (see, e.g.,Bastian S et al., Metab. Eng. 2011; 13(3):345-52). Two mutants of IlvC(A71S, R76D, S78D, Q110V/A) with higher activity with NADH were chosento replace wild-type IlvC in plasmid pYX90 (see, FIG. 11A-11B).

Improved Fusel Butanol Yield Under Anaerobic Fermentation with NADPH:

We hypothesized that cofactor imbalance compromised fusel butanol yieldduring protein bioconversion. To test this hypothesis, the nativecofactor NADPH of YqhD and IlvC was added into the fermentation mediumas an external source of NADPH. FIG. 12A-12B show that addition of NADPHsignificantly improved yields of isobutanol and 2/3-methyl-butanolduring protein bioconversion. Within 5 days of cultivation, yields ofisobutanol, 2/3-methyl-butanol, and total fusel butanol increased byabout 34%, 28%, and 30%, respectively, confirming that cofactorimbalance can be one factor affecting fusel butanol production.

Bioconversion of Amino Acid Mixtures and Algal Protein into FuselButanol:

The fusel butanol yields of the engineered YH83 strains, which containedboth IlvC and YqhD mutants, were initially investigated throughbioconversion of amino acid mixtures in the 1×M9 medium. As seen in FIG.13A, the mutant strains produced various amounts of fusel butanol in thefermentation broth. Among the seven mutant strains, four strains (AY1,AY3, VY3, and VY5) yielded at least 30% higher concentrations of fuselbutanol, as compared to wild-type. In particular, the AY3 strainproduced more than 60% higher amount of fusel butanol than wild-type,i.e., up to 6 g/L fusel butanol from 20 g/L amino acids. The wild-typeproduced 3.7 g/L fusel butanol.

Further studies were conducted with pretreated algal proteinhydrolysates. Two hydrolysates were used as medium to investigatefermentation performance of mutant strain AY3. As shown in the FIG. 13B,mutant strain AY3 produced higher titers of isobutanol,2/3-methyl-butanol, and total fusel butanol with both pretreated algalprotein hydrolysates (ATP3 and ODU), as compared to wild-type strainYH83.

Within 3 days of fermentation, the mutant strain AY3 yielded more than100% and 38% higher total fusel butanol titers than wild-type with ATP3and ODU, respectively, as shown in FIG. 13B. Yields using algalhydrolysates were lower than that observed with amino acid mixtures.Yields can be optimized, e.g., by providing supplemental nutrients withthe algal hydrolysates, adjusting the ionic strength of the hydrolysate,neutralizing the hydrolysate, etc.

As shown in FIG. 13C, only about 25% of algal protein hydrolysates wereconsumed after 3 days of fermentation. Based on substrate consumption,the strain AY3 yielded 0.2 to 0.18 g fusel butanol/g amino acid forconverting algal hydrolysates AY3 and ODU, respectively. Yields could beoptimized in any useful manner, e.g., by increasing incubation times,increasing protease digestion times, repeating and recycling separatedfractions, etc.

Here, we engineered two enzymes (IlvC and YqhD) in the isobutanolbiosynthesis pathway to resolve cofactor imbalance during fermentation.By combining beneficial mutations of these two enzymes, the engineeredAY3 strain improved fusel butanol yield with an algal hydrolysate, ascompared to the wild-type strain. Fusel butanol possess the higherenergy density, lower vapor pressure, lower hygroscopicity than fuelethanol and has been considered as an advanced fuel compounds (see,e.g., Lan E I et al., “Microbial synthesis of n-butanol, isobutanol, andother higher alcohols from diverse resources,” Bioresour. Technol. 2013;135:339-49; and Smith K M et al., “An evolutionary strategy forisobutanol production strain development in Escherichia coli,” Metab.Eng. 2011; 13(6):674-81). Recently, algal protein hydrolysates werereported into fusel butanol but at a relative low titer (see, e.g., HuoY X et al., Nat. Biotechnol. 2011; 29(4):346-51). One of possiblefactors that results in the lower fusel titer could be the co-factorimbalance during the fermentation, in which strategies to address thesefactors are described herein.

Other Embodiments

All publications, patents, and patent applications mentioned in thisspecification are incorporated herein by reference to the same extent asif each independent publication or patent application was specificallyand individually indicated to be incorporated by reference.

While the invention has been described in connection with specificembodiments thereof, it will be understood that it is capable of furthermodifications and this application is intended to cover any variations,uses, or adaptations of the invention following, in general, theprinciples of the invention and including such departures from thepresent disclosure that come within known or customary practice withinthe art to which the invention pertains and may be applied to theessential features hereinbefore set forth, and follows in the scope ofthe claims.

Other embodiments are within the claims.

The invention claimed is:
 1. A method of upgrading a biomass, the method comprising: pre-treating the biomass with one or more acids, thereby providing one or more biocomponents comprising one or more carbohydrates; fermenting the one or more carbohydrates with a first genetically engineered organism, thereby providing a first fermentation product comprising an alcohol, wherein the first genetically engineered organism is selected from the group consisting of E. coli KO11, E. coli LY01, E. coli SZ110, E. coli LY168, Z. mobilis AX101, S. cerevisiae 424A(LNH-ST), and A cerevisiae ATCC 96581; separating the alcohol from the first fermentation product, thereby providing a separated fermentation portion; treating the separated fermentation portion with one or more enzymes, thereby providing an enzymatically treated portion comprising an amino acid; and fermenting the amino acid in the enzymatically treated portion with a second genetically engineered organism, thereby providing a second fermentation product comprising an alcohol and an amine, wherein the second genetically engineered organism comprises: a modified alcohol dehydrogenase or a nucleic acid encoding the modified alcohol dehydrogenase, wherein the modified alcohol dehydrogenase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO:4 having Ile, Tyr, Val, Leu, or Phe at position 39; and Pro, Arg, His, Lys, or Trp at position 40, and wherein the modified alcohol dehydrogenase has an increased reactivity with nicotinamide adenine dinucleotide (NADH), as compared to a wild-type alcohol dehydrogenase; and a modified ketol-acid reductoisomerase or a nucleic acid encoding the modified ketol-acid reductoisomerase, wherein the modified ketol-acid reductoisomerase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO:6 or 7, and wherein the modified ketol-acid reductoisomerase has an increased reactivity with NADH, as compared to a wild-type ketol-acid reductoisomerase.
 2. The method of claim 1, further comprising: separating the alcohol from the second fermentation product, thereby providing a further separated fermentation portion; and lyophilizing the further separated fermentation portion, thereby providing one or more amino acids.
 3. The method of claim 1, wherein the modified ketol-acid reductoisomerase comprises a polypeptide sequence having at least 90% sequence to the amino acid sequence of SEQ ID NO:
 7. 4. A method of upgrading a biomass, the method comprising: pre-treating the biomass with one or more acids and/or one or more enzymes, thereby providing one or more biocomponents; fermenting the one or more biocomponents with a genetically engineered organism comprising a modified alcohol dehydrogenase and a modified ketol-acid reductoisomerase, thereby providing a fermentation product, wherein the modified alcohol dehydrogenase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO:4 having Ile, Tyr, Val, Leu, or Phe at position 39; and Pro, Arg, His, Lys, or Trp at position 40, wherein the modified alcohol dehydrogenase has an increased reactivity with nicotinamide adenine dinucleotide (NADH), as compared to a wild-type alcohol dehydrogenase, wherein the modified ketol-acid reductoisomerase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO:6 or 7, and wherein the modified ketol-acid reductoisomerase has an increased reactivity with NADH, as compared to a wild-type ketol-acid reductoisomerase; separating one or more alcohols from the fermentation product, thereby providing a separated fermentation portion; and lyophilizing the separated fermentation portion, thereby providing one or more amino acids.
 5. The method of claim 4, wherein the modified ketol-acid reductoisomerase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO:
 7. 6. The method of claim 1, wherein the biomass comprises distillers grain, an oilseed meal, a feed, or a cereal by-product.
 7. The method of claim 1, wherein the alcohol is selected from the group consisting of ethanol, propanol, butanol, and alkylated formed thereof.
 8. The method of claim 1, wherein the one or more acids comprises hydrochloric acid or sulfuric acid.
 9. The method of claim 1, wherein the one or more enzymes comprises one or more proteases.
 10. The method of claim 1, wherein the modified alcohol dehydrogenase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 4 having Ile at position 39 and Arg at position 40; or Tyr at position 39 and His at position
 40. 11. The method of claim 1, wherein the modified ketol-acid reductoisomerase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 7 having Ser or Thr at position 71, Asp or Glu at position 76, Asp or Glu at position 78, Val or Ala or Leu or Ile at position 110, Gly or Ala at position 146, Arg or Lys at position 185, and Glu or Asp at position
 433. 12. The method of claim 1, wherein the modified ketol-acid reductoisomerase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 6 and having the following mutations of A71S, R76D, and S78D.
 13. The method of claim 12, wherein the polypeptide sequence of the modified ketol-acid reductoisomerase further comprises the mutation of Q110V or Q110A.
 14. The method of claim 4, wherein the modified alcohol dehydrogenase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 4 having Ile at position 39 and Arg at position 40; or Tyr at position 39 and His at position
 40. 15. The method of claim 4, wherein the modified ketol-acid reductoisomerase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 7 having Ser or Thr at position 71, Asp or Glu at position 76, Asp or Glu at position 78, Val or Ala or Leu or Ile at position 110, Gly or Ala at position 146, Arg or Lys at position 185, and Glu or Asp at position
 433. 16. The method of claim 4, wherein the modified ketol-acid reductoisomerase comprises a polypeptide sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 6 and having the following mutations of A71S, R76D, and S78D.
 17. The method of claim 16, wherein the polypeptide sequence of the modified ketol-acid reductoisomerase further comprises the mutation of Q110V or Q110A. 